Partners
by TrulyyScrumptious
Summary: It's 2016 and Mulder and Scully have been back at the Bureau for almost a year. They are at a stand still with the new syndicate, that is until Agent Booth and his partner Dr. Brennan show up in the office with a case.
1. This Cannot Be What It Looks Like

Chapter One: This Cannot Be What It Looks Like

 **September 12** **th** **, 2016.**

 **9:30 p.m.**

 **Washington D.C.**

 **F.B.I. Headquarters.**

The sound of Booth's ringtone echoed in the office, and he reached over to answer the phone,

"Go for Booth." Sealy said as he listened to another's agent's voice over the receiver. "Alright, Bones and I will be there in 30 minutes," he said hanging up the phone. Booth hit number one on his keypad and speed dialed his wife, "Bones, we've been given a new case." Bones spoke from her office, "No, the Jeffersonian is on the way. I'll swing by and pick you up. See you soon." Booth hung up the phone, and grabbed his jacket as he exited the office to go pick up his partner.

 **September 12** **th** **, 2016**

 **10:05 p.m.**

 **Five Miles Outside Washington D.C. City Limits.**

The pair pulled up to the crime scene, and got out of their black SUV. Police sirens lit up the open field around them in blue and red lights. About fifteen police officers were already on the scene as they walked up, and ducked under the yellow crime scene tape. Bones noticed the confused look on the officers faces around her as she walked through the crime scene. The pair went over to the officer who was in charge,

"I'm Agent Booth, this is my partner Dr. Temperance Brennan," Sealy said flashing his F.B.I. badge.

"I'm glad the two of you showed up," the officer said in relief. Bones and Booth looked at each other in confusion,

"I don't quite understand why you wanted the F.B.I. on this case," Bones said placing her hands in her coat pockets. "In fact, the details about the murders seem quit vague," Bones admitted. In the car, Booth had said that they would understand why the two of them were called when they arrived.

"We called in the F.B.I., because we have never seen anything like this before." He continued, "I was told that you two had one of the best closure rates in the Bureau, and I didn't think we could solve this on our own." Curiosity flashed across both their faces, as Booth looked over at his partner.

"Why don't you just show us the bodies," Booth said letting Bones take the lead in front of him.

"Alright, this way," the officer turned, and pushed past a small crowd of other cops who made way for the new comers.

As soon as the cops parted for Booth and Brennan to get by, the pair saw what was causing a stir amongst the police at the scene. In the middle of the field was a completely charred body that still had smoke rising off of it.

Brennan stepped closer to the body and kneelt down beside it. The burning on the victim was not like any other case she had worked on previously. There seemed to be no point of origin for the start of the fire on the body. The area around the body was undisturbed, which meant it was moved at some point to this location. Brennan also noted that in this deeply charred state that this body would have fallen apart upon being moved. Which led her to the thought of spontaneous combustion, but she knew logically that this was implausible. Temperance's scientific mind was aware that there had to be a point of origin, it just wasn't obvious with the naked eye.

She stood looking at Booth,

"This is interesting," Brennan confessed.

"Well, this is just the tip of the ice burg," the lead officer stated.

"You mean there is more?" Booth asked. The officer nodded,

"This way."

He took them about fifty yards farther into the middle of the field. Several orange flags stuck out like beacons, making it clear where the next crime scene was. As soon as the long time partners caught sight of the next body, the pair stopped in their tracks upon seeing what lay before them. Like the scene behind them there was a dead body lying in the grass, but with some distinct differences. Unlike like previous body this one was not burned, but was still shocking none the less. The face of this victim was mutilated beyond recognition; all the orifices on his face were closed as if sealed off to keep something out. But, this is not what caught Bones and Booth's full attention. What had both of their attention lay two yards from the outreached hand of the body.

A metal container, about three feet by two feet, was located on the ground at both of their feet. In that container is what Booth and Brennan now realized had all of the officers in a buzz.

Booth took his wife by the elbow and pulled her aside,

"Bones, uh," he looked back at the container, "I know this cannot be what it looks like."

Brennan nodded her head in agreement,

"Well, of course it's not. If you suggested that what is lying on the ground back there is really an…." She was cut off by Booth.

"I know it's not what everyone here thinks it is, but," he paused, "we do have a special division dedicated to this type of case."

"Wait, you do," Bones laughed, "I cannot believe that the F.B.I. would waste resources on a division such as that."

"Actually, the division just re-opened after several years of being shut down," Booth replied.

"Who would want to work these types of cases on a daily basis?" she questioned with a disapproving look.

"Actually, the two agents who worked in the division before it was shut down some years back. For some reason they were asked by an assistant director to come out of hiding and to come back to the F.B.I."

"Out of hiding?" Bones questioned. "Why would they be in hiding?" Booth hesitated before answering. Sealy knew all the rumors that swirled around the two agents that used to work the strange division, and he honestly didn't know what was fact and what was fiction.

"They were both technically fugitives at one point back in the early 2000's. I don't know all the details, but that matter has been cleared up, and they are no longer running from the F.B.I."

"And knowing all of this you want us to work with these people?" Bones said raising an eyebrow.

"They are experts with the para-normal phenomena. Plus," he half smiled, "I've always wanted to go down to the basement."

"The basement?" Brennan shook her head, "Who are these people?"

"Well, they are a little spooky, but I would be lying to you if I said I never thought about working an actual X-File."

"An X-File?" Bones sighed, "Oh, brother."


	2. Are You Seeing What I'm Seeing?

Chapter Two: Are You Seeing What I'm Seeing

 **September 13** **th** **, 2016.**

 **10:00 a.m.**

 **Washington D.C.**

 **Basement of the F.B.I. Headquarters.**

"Scully, remind me why we agreed to work for the F.B.I. again?" Mulder asked as he threw a sharpened pencil up at the ceiling.

"Because, we discovered that the shadow government we have been chasing after all these years has reemerged, and as crazy as it sounds they may be conspiring to release a virus to wipe out the human race," Scully answered in an even tone.

"I knew there was a good reason. Just needed a little reminding," he started to throw another pencil at the ceiling before Scully interrupted.

"Would you stop that?" she gave him a disapproving glance. "We have actual work to do, Mulder."

"Not two nights ago we were the almost assassinated by three men, after a virtual Langly reached out to us through my phone. I think we can take it easy for one day. Plus," he smiled "it means we can spend some alone time together in the office." Mulder winked across the room at her, "Just like old times."

Before she could respond a knock came from the door. The two agents looked at one another in slight confusion. No one ever came down to the basement, let alone to see the two of them. Scully moved over next to Mulder's desk and called out,

"Come in."

The door opened and a man and a woman entered the room.

"Fox Mulder and Dana Scully?" the man asked.

"Yes, I'm Agent Scully, and this is my partner Agent Mulder," Scully replied pointing over at Fox. She noticed the case file in his right, and looked over at her partner who glanced up at her from his seat.

"I'm Agent Sealy Booth, and this is Doctor Temperance Brennan of the Jeffersonian Institution." Booth walked over and extended a hand to Scully and then Mulder, both shaking his hand politely. He started to speak, but was interrupted by his partner behind him,

"Interesting office you have here," she walked around the room analyzing her surroundings. Her eyes stopped momentarily at the poster behind Agent Mulder's head.

"We like it, "Mulder responded giving Scully a sideways look that said, "Who are these people?"

"I'm curious as to why the two of you work in the basement. It cannot be out of convenience? Do you not work well with others?" She looked between Mulder and Scully with a serious expression on her face.

"It is not that we do not work well with others, Dr. Brennan," Scully stated. "It is that people in the bureau do not take the cases we work on seriously, nor do they see the importance of our work." From his chair Mulder beamed up at his partner with pride as she spoke. Mulder's display did not go unnoticed by Bones or Booth.

Before Scully could say anything more Agent Booth interjected,

"I apologize for Bones," he looked back at her over his should, "she can be very blunt."

The nickname Booth called his partner rang a bell in Mulders mind,

"Wait a sec, I know you guys. You two are the F.B.I. hot shots who have captured the Gravedigger killer?"

"I am actually not an F.B.I. agent but, yes, you are correct," Bones replied. "We have caught a number of high profile serial killers," she looked over at her partner with a smile. It was now Mulder and Scully's turn to notice the look shared between the two partners.

"Since you know about our reputation at the bureau, it's only far I tell you that we know a little something about yours as well," Booth said moving to stand next to Bones.

"Is that so," Scully inquired.

"Yes," Booth continued. "That's actually why we are here. We were handed a case last night by local D.C.P.D. that is what you two might consider," he paused and looked at his partner, "extra-terrestrial. I thought since little green men were your specialty, the two of you would want to help us out on the case."

The mention of extra-terrestrials peaked the interest of the two older agents.

"What type of little green men did you find last night?" Mulder asked.

"Well, take a look for yourself," Booth handed Mulder the case file.

Mulder opened the file,

"Scully," he whispered, "Are you seeing what I'm seeing?"

"Oh, my god," Scully looked down at her partner with a worried expression. "I thought we would never find this again."

"Neither did I, Scully."

The picture that was displayed in front of them was of a metal canister, one that both agents had seen before. In the picture, trapped behind the behind clear glass of the canister was a small grey alien, and on the bottom of the canister the words "Purity Control" were written. This was the same alien life form that Scully had given to Deep Throat in exchange for Mulder's life back in 1993.

"Where did you find this?" Mulder asked.

"In a field about five miles outside the city," Booth answered looking at his partner with a confused expression.

"I'm assuming that you have seen what is in those pictures before?" Bones asked as Mulder shuffled through the remaining photos. He held one in particular up for him and his partner to examine; it was the photo of the faceless man,

"We need to see these bodies right now," Mulder said standing up, "You have no idea what you just found."


	3. You're A Doctor?

Chapter Three: You're A Doctor?

 **September 13th, 2016.**

 **10:45 a.m.**

 **Washington D.C.**

 **Jeffersonian Institution.**

Fox and Dana followed behind Agent Booth and Dr. Brennan as they walked up the steps of the Jeffersonian. Scully had heard a lot about the establishment, and if she was being honest she had always wanted to explore the laboratories of this institution. Being a doctor she was highly curious as to what high tech equipment was being used inside these walls. The Jeffersonian had a reputation for hiring the brightest minds in the scientific field, and if she wasn't working on the X-Files a place such as this would be on Scully's radar.

The long time partners followed behind the younger pair as they entered the building and onto an elevator. Mulder looked down at Scully and noticed the slight smile on her face as the elevator climbed. The metal doors dinged and they exited to metal box. The pair followed Bones and Booth down a long hall before they turned left coming face to face with large glass doors. Bones pulled a key card from her pocket and swiped it through the security reader. The light on the box turned green, and the doors in front of them clicked open as they walked into the lab. As soon as Scully entered the facility her mouth fell slightly open,

"This is amazing," she stated looking around in awe.

"Yes, it is," Bones said with a smile. "Our facility is state of the art."

"I can tell," Scully replied looking at all of the lab equipment as she walked through the lab, "If the F.B.I. had this type of equipment at their disposal, I don't think I'd ever leave the lab," Scully said looking up at Mulder. He now understood why she had a smile on her face in the elevator. This place was basically Disneyland for Scully. Mulder looked away from his partner with a frown. Mulder knew that if it wasn't for him and his crusade, Scully would likely be working at an institution such as this. Deep down he always knew that working on the X-Files was holding Scully back from her true potential as a medical doctor. Mulder's thoughts were interrupted as Bones looked back at Scully,

"You're a doctor?" Dr. Brennan sounded a bit shocked as she spoke.

"Yes, I'm a medical doctor," Scully confirmed.

Mulder noted the surprised look Bones gave her partner.

"What do you have your medical degree in, Dr. Scully?" Bones asked with a hint of respect in her voice.

"Forensic Pathology." Scully said with confidence. Mulder was beginning to realize that science and IQ was what really matter inside of this lab.

From somewhere in the lab someone shouted "King of the lab, baby," and both Bones and Booth laughed. Mulder looked at Scully and mouthed "King of the lab," she looked back at him and shrugged.

The pair followed behind Bones and Booth into the autopsy room,

"Well, here are your bodies," Booth said gesturing toward the two covered forms lying on cold metal tables.

"I'm going to need to preform autopsies on both of these bodies," Scully said moving closer to the bodies before Dr. Brennan stepped in front of her,

"We have our own pathologist who can perform the autopsy."

Scully stood up straight and crossed her arms over her chest,

"If I am not mistaken, you brought us on this case to help you out. I am more than capable of performing these autopsies on my own. And," she stepped forward, "As good as your pathologist may be, they won't have any idea what they are looking for, and I do."

Dr. Brennan considered her statement for a moment before stepping aside,

"I would like to observe your autopsy," Brennan paused, "If you do not mind. I am curious as to what you think you might find."

"You are more than welcome to stay but," she turned to Mulder and Booth, "I do not need an audience." And before the two men left she said, "Where is the unidentified specimen you found at the crime scene?"

"It's in a different part of the lab," Booth answered.

"I'd like to take a look at that," Mulder replied. Booth nodded and led the way out of the room.

Bones and Scully changed into gowns and masks in silence. Bones was not quite sure what to think of the smaller redhead as she placed latex gloves over her hands. She was obviously not afraid of a challenge, and from what Bones gathered so far, Scully was a lot smarter than Bones originally gave her credit for.

Scully made her way over to the first body and pulled back the sheet. The faceless man that was revealed did not shock the redheaded in the slightest,

"You do not seem bothered by this man's appearance," Bones said watching her closely.

"I've worked on more odd cases than you could possibly image. This is not the strangest thing I have ever seen," Scully said glancing up at the brunette before making her way to the other corpse. Scully pulled the sheet back, and Bones noticed the redhead clench her jaw slightly before covering up the corpse again.

Seeing the burned body brought back memories of Casandra Spender, and how she had died in a similar fashion. It was also not lost on Scully that she had once almost been killed in a similar way.

"I cannot perform an autopsy on that body, it is far to burned. I'll need to call in a forensic anthropologist," Scully said making her way back to the first body.

"No need," Dr. Brennan stated, "I'm a forensic anthropologist. I'll be examining the body."

"Aren't most forensic pathologist out sifting through dirt in search for old bones," it was Scully's turn to get a small dig in. Bones watched as Scully performed the Y-incision on the body with perfect technique,

"I deserved that," she said in a monotone. "But, yes, you are correct. Most people in my field are digging up old bones, and not helping the F.B.I. solve crimes." Across the table Scully continued her autopsy as talked,

"How did you end up here?"

"It was not something I planned. I had just come back from an excavation mission in South America, and was asked to work on a case with Booth," Scully noticed the smile on her face when she talked about her partner. "We actually did not get along at first, but we made a great team. After we solved the case realized I there was a whole side of my field that I was missing out on," she leaned back as Scully began removing organs. "I am not what you call a "people person" so I had a hard time at first interacting with actual living people. Being out in the field with skeletons for years on end doesn't exactly build social skills."

"You don't seem to have much of a problem with people now," Scully placed an internal organ on the scale, "Beside from being rather blunt."

"If it wasn't for Booth I probably would have left a long time ago. He has helped me grow as a person more than I could have ever possibly imagined. And, I apologize for underestimating you," Bones said, "I just was a little thrown as to why a medical doctor, who seems to have great skill, would be working in a unit such as the X-Files."

Scully stopped what she was doing for a moment so she could answer,

"Most people see what Mulder and I do as a joke. No one takes what we have to say seriously because we chase after aliens. When I first started working with Mulder, I did not believe in the work. I thought The X-Files was a ridiculous division, but I came to found out that not everything we investigated was just a write off case. Now, unlike my partner I do not believe every ghost story I am told. I need scientific proof, which makes some of the cases we work on together rather difficult. Especially, when Mulder goes around asking people if they have seen Big Foot," Scully smiled and rolled her eyes. "But, we have uncovered things that other people have tried very hard to cover up."

"You are talking about government conspiracies?" Bones questioned as Scully began her work on the body again.

"I know it sounds implausible, but there are forces in our government that control so much more than you could ever possibly imagine."

"You are right, that does sound implausible," Bones stated.

"I used to think that too," Scully said in a low voice and continued her work.

Scully removed and weighed several more organs before speaking again,

"So, you and Booth seem rather close," she asked with slight curiosity.

"Our partnership isn't exactly what you call conventional, considering the fact that we are married and have two children," Bones proclaimed.

Scully looked up from her work,

"Isn't that against F.B.I. regulations?"

"Well, like I said before, I don't work for the F.B.I." Brennan smiled.

"How long have you two been married?" Scully asked.

"For three years, but we were together for two years before that," Bones said looking down at where her wedding ring would be if didn't have on autopsy gloves.

"And, how long have you been working together?" Scully asked.

"Eleven years."

It did not go unnoted by Scully at how much she and Brennan had in common when it came to their partnerships.

"Are you married Agent Scully?" Brenna asked her with a slightly raised eyebrow.

"You can call me, Dana."

"Alright, Dana," Bones confirmed, "And please call me Temperance."

"And no I am not married." Scully answered noticing her raised eyebrow. "I've never been married actually."

Temperance looked from Scully to a spot across the lab. Scully looked up to where Bones had looked, and saw it was where Mulder and her partner were standing.

"Did you think that Mulder and I were together?" she asked not looking up at Temperance. The room was quiet for a moment,

"Actually, yes. It did not go unnoticed by me the way the two of you gaze at one another," Bones stated in her bluntness.

"I do not gaze at Mulder, Temperance," she shot back.

"If you say so, Dana," Temperance smiled. "But, people do not go on the run with just anyone."

"You know about that?" Dana asked as she kept performing her autopsy.

"Yes, the two of you have quiet the reputation at the bureau," Temperance answered.

"Our reputation never bothered us," Dana kept silent for a few moments before she spoke again, "And, you weren't exactly wrong. Mulder and I were together, but not anymore," Scully confirmed.

"And, yet you agreed to come back to the F.B.I., and work together with him again?" Brennan countered.

"Like I said before, our work is very important. And we have always been partners before anything else, that has never changed."

Brennan respected the level of trust Scully seemed to place in her partner. She knew the type of connection you could build with a person with that level of trust.

"Can I give you some advice?" Temperance asked.

Scully considered her question for a second,

"Yes."

"I do not know what happened between the two of you, but you both obviously still care for one another," Brennan continued, "Don't ignore it. Especially, if you mean as much to one another as I think you do."


	4. They Are Quite The Pair

Chapter Four: They Are Quite The Pair

 **September 13th, 2016.**

 **12:02 p.m.**

 **Washington D.C.**

 **Jeffersonian Institution.**

After Temperance gave Scully her advice, the conversation stuck mainly to previous cases the two women had worked on. Scully found that she rather liked the forensic anthropologist. It was impressive how someone could completely change career paths, and start working with the F.B.I. to solve murder cases. Dana could relate to Dr. Brennan's career change, though Scully's came much earlier in life than Temperance's did. But, Scully's career change is something she did not regret. The secrets she had helped uncover, and the lives she had saved due to her work on the X-Files were worth every second she spent in that basement. She also would not trade a minute of working with Mulder for the world, something she hoped he knew.

Scully knew she did not vocalize how much Mulder meant to her enough. Maybe, she thought, that's one of the reasons she no longer slept next to him every night. Scully admitted it was both of their faults why they were not together anymore. It had been almost a year and a half since Dana left Mulder, but she knew it was the right thing to do. Mulder had started to go down a dark hole that not even she could pull him out of. In the end she had to leave, if only to make him realize that he needed to pull himself out of the dark place he had fallen into. Since they had started working on The X-Files again, Dana realized how much she missed being around him. She longed for Mulder to hold her in his arms again, and she knew he wanted her to come home.

"Did you find what you were looking for?" Temperance asked interrupting Dana's train of thought.

"Yes," Scully answered as she covered the body with a white sheet, "and also no." Dana peeled off her gloves and gown before throwing them into a waste bin. "I need to talk to Mulder."

Temperance nodded knowing Scully would not tell her what she found until after she talked with her partner. The redhead stayed behind as Brennan went into her office, where Booth and Mulder sat chatting on the couch. Bones noticed both men smiling as she entered,

"Agent Mulder, your partner would like to speak with you."

Mulder got up,

"Thanks," he looked back at Booth. "We will continue this conversation later."

Booth smiled and gave him a thumbs up as Mulder left the room to find his partner.

"Seems the two of you were getting along well," Bones stated.

"Ya," he replied running a hand through his hair, "he is not what I expected at all. I mean, the whole I believe in aliens thing is bizarre, but he's not a bad guy." Booth stood crossing the room to stand in front of his wife, "What about Agent Scully? What do you think of her?"

"She is quite fascinating actually, and much smarter than I previously thought. From what I can tell her and Mulder have nothing in common, but that doesn't seem to affect their partnership in the slightest."

Booth tilted his head,

"From what I have heard about them, their ability to solve cases rivals our own."

"Is that so?" Bones said raising an eyebrow.

"I was curious about their closure rate, so while Mulder was looking around the lab I looked it up on the F.B.I. database," he paused.

"And?" Bones urged him to finish.

"Since they started working together in '93, their closure rate averages just above 80%," Booth concluded.

"That's higher than ours," Bones said in a shocked tone.

"I know. I couldn't believe it," Booth exclaimed raising his hands in the air, "Those two are nothing like I was led to think at the bureau."

"They are quite the pair," Bones agreed. "In more ways than one," she added.

"You caught onto that too?" Booth asked.

"Of course," Bones said knowingly. "We both know how observant I am. I'm just surprised you caught on as well."

"Why wouldn't you think I'd catch that?" He said in a slightly defensive tone.

"Because, you are usually so focused on a case that you sometimes overlook small details," Bones said with a shrug. "Plus, you are not one to pry into other people's personal lives."

"Well, that is true," Booth said about the latter. "But, who could miss the way those two make googly eyes at each other." They both laughed,

"You mean the way we used to make googly eyes at each other," she smiled.

"Exactly same way we looked at each other," Booth replied closing the space between them. He wrapped one arm around his wife's waist, pulling Bones close against him as he kissed her sweetly on the lips. After a moment they pulled away from each other slightly,

"The same way we _still_ look at each other," She corrected, and leaned in for another kiss.

 **The Autopsy Room.**

Mulder entered the room and found Scully leaning against the sink in the back of the room.

"What did you find, Scully?" Scully stared back at him with a look that told Mulder, he wasn't about to hear what he wanted,

"He's not what you think," she said pointing to the body that was just autopsied. "That man is completely human. We never should have thought otherwise."

"Why is that?" Mulder inquired.

"Because, if this person really was part of the alien resistance," she let out a sigh, "he would have disintegrated into a puddle of green goo. We were so quick to jump on this case we overlooked that detail."

Mulder hung his head, kicking himself mentally for not picking up on that detail before,

"Guess we are still a little rusty. I wouldn't have over looked that detail fifteen years ago."

"I missed it too, Mulder," she moved over and placed a reassuring hand on his arm. "But, the burning and the facial mutilation do coincide with the alien resistance. So, we do have an X-File on our hands."

"And," Mulder added, "There is still a little grey alien locked up in a freezer in this facility." Scully looked up at him and nodded,

"Yes, there is."


End file.
